What species are in the swath data?
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SP_CODE
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SPECIES
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AGCL
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Agarum clathratum
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ALES
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Alaria esculenta
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ANSP
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Anomia
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APPA
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Aplidium pallidum
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ASDI
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Ascophyllum nodosum
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BLD
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UNID Juv Laminariales
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BOHA
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Bonnemaisonia hamifera
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BOSC
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Botryllus schlosseri
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BOVI
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Botrylloides violaceus
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BUSP
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Bugulina spicata
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BUTU
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Crisularia turrita
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CF
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Crepidula fornicata
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CHCR
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Chondrus crispus
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CIIN
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Ciona intestinalis
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CISA
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Ciona savignyi
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CLCI
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Clathromorphum circumscriptum
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CLSP
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Cliona
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CO
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Corallina officinalis
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COF
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Codium fragile
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COPE
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Colpomenia peregrina
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COTR
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Coccotylus truncatus
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CREB
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Crisia eburnea
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CRSP
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Ceramium
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CYPU
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Cystoclonium purpureum
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DEAC
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Desmarestia aculeata
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DECA
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Dendrodoa carnea
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DEMU
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Dendrobeania murrayana
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DEVI
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Desmarestia viridis
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DIAL
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Didemnum albidum
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DIAT
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Diatom Tube Mat
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DIP
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Diplosoma listerianum
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DIVE
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Didemnum vexillum
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DUCO
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Dumontia contorta
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EC
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Encrusting coralline
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EUCR
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Euthora cristata
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FG
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Filamentous Green
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HADU
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Halisarca dujardinii
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HAPA
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Halichondria (Halichondria) panicea
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HATO
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Halosiphon tomentosus
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HIRU
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Hildenbrandia rubra
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HJ
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Dasysiphonia japonica
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HYSP
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Hymedesmia
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ISAL
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Stenosemus albus
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ISRU
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Boreochiton ruber
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LADI
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Laminaria digitata
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LESP
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Leptophytum acervatum
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LEUC
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Leucosolenia
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LIGL
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Lithothamnion
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LISP
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Lithophyllum
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LIVE
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Patinella verrucaria
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MAST
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Mastocarpus stellatus
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MEMA
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Membranipora membranacea
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MOMO
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Modiolus modiolus
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MYED
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Mytilus edulis
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OBSP
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Obelia
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OSED
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Ostrea edulis
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PAPA
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Palmaria palmata
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PHRU
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Phycodrys rubens
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PHSP
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Phymatolithon
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POLS
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Polysiphonia
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PORO
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Polyides rotunda
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PORS
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Porphyra
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PTSE
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Ptilota serrata
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RAT
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Red Algal Turf
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SADE
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Saccorhiza dermatodea
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SCUN
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Schizoporella unicornis
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SE
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Thylacodes
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SL
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Saccharina latissima
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SLJ
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Saccharina latissima
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SPRE
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Spermothamnion repens
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TETE
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Testudinalia testudinalis
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TISP
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Titanoderma
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TRIN
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Tricellaria inopinata
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TUV
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Tubular Ulvoid
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UEC
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Unidentified Erect Coralline
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UFR
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Unidentified Filamentous Red
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URB
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Unidentified Red Blade
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UV
|
Blady Ulvoid
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Let’s Plot Trends
Here are some functions we’ll apply to each species. I’ll then fit mixed models with all of them using
COUNT ~ YEAR * SITE + (1|TRANSECT)
with a gaussian error. Note, it’s count, so, I could use Poisson, but, that needs to be way more tuned to each model - this should be fine for a first cut?
Here’s how we’ll do it:
tseries_plot <- function(adf){
ggplot(adf,
aes(y = PERCENT_COVER, x = YEAR,
color = TRANSECT)) +
geom_point() +
geom_line() +
facet_wrap(~SITE, nrow = 2) +
labs(color = "Transect",
y = "Percent Cover", x = "Year",
title = adf$SPECIES[1])
}
tseries_fun <- function(adf){
glmmTMB(PERCENT_COVER/100+0.001 ~ YEAR * SITE,
data = adf,
family = beta_family())
}
generate_output <- function(adf){
cat(paste0("## ", adf$SP_CODE[1], " ", adf$SPECIES[1], " \n<br>"))
tseries_plot(adf) %>% print()
if(sum(adf$PERCENT_COVER>10) > 15){
tseries_fun(adf) %>%
car::Anova(test.statistic = "Chisq") %>%
tidy() %>%
knitr::kable("html", digits = 3) %>%
kableExtra::kable_styling() %>%
print
}
cat("\n\n")
}
Now let’s purrr::walk() through the whole shebang.
walk(split(upc, upc$SP_CODE), generate_output)
AGCL Agarum clathratum

ALES Alaria esculenta

ANSP Anomia

APPA Aplidium pallidum

ASDI Ascophyllum nodosum

BLD UNID Juv Laminariales

BOHA Bonnemaisonia hamifera

BOSC Botryllus schlosseri

BOVI Botrylloides violaceus

BUSP Bugulina spicata

BUTU Crisularia turrita

CF Crepidula fornicata
## Registered S3 methods overwritten by 'car':
## method from
## influence.merMod lme4
## cooks.distance.influence.merMod lme4
## dfbeta.influence.merMod lme4
## dfbetas.influence.merMod lme4
|
term
|
statistic
|
df
|
p.value
|
|
YEAR
|
100307.541
|
1
|
0
|
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SITE
|
2158.400
|
2
|
0
|
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YEAR:SITE
|
2269.389
|
2
|
0
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CHCR Chondrus crispus
|
term
|
statistic
|
df
|
p.value
|
|
YEAR
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54575.43
|
1
|
0
|
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SITE
|
15435.08
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2
|
0
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YEAR:SITE
|
14959.07
|
2
|
0
|
CIIN Ciona intestinalis

CISA Ciona savignyi

CLCI Clathromorphum circumscriptum

CLSP Cliona

CO Corallina officinalis
|
term
|
statistic
|
df
|
p.value
|
|
YEAR
|
19046.305
|
1
|
0
|
|
SITE
|
6465.974
|
2
|
0
|
|
YEAR:SITE
|
6235.354
|
2
|
0
|
COF Codium fragile

COPE Colpomenia peregrina

COTR Coccotylus truncatus

CREB Crisia eburnea

CRSP Ceramium

CYPU Cystoclonium purpureum

DEAC Desmarestia aculeata

DECA Dendrodoa carnea

DEMU Dendrobeania murrayana

DEVI Desmarestia viridis

DIAL Didemnum albidum

DIAT Diatom Tube Mat

DIP Diplosoma listerianum

DIVE Didemnum vexillum

DUCO Dumontia contorta

EC Encrusting coralline

EUCR Euthora cristata

FG Filamentous Green

HADU Halisarca dujardinii

HAPA Halichondria (Halichondria) panicea

HATO Halosiphon tomentosus

HIRU Hildenbrandia rubra

HJ Dasysiphonia japonica
|
term
|
statistic
|
df
|
p.value
|
|
YEAR
|
31440.697
|
1
|
0
|
|
SITE
|
1835.231
|
2
|
0
|
|
YEAR:SITE
|
1830.743
|
2
|
0
|
HYSP Hymedesmia

ISAL Stenosemus albus

ISRU Boreochiton ruber

LADI Laminaria digitata

LESP Leptophytum acervatum

LEUC Leucosolenia

LIGL Lithothamnion

LISP Lithophyllum

LIVE Patinella verrucaria

MAST Mastocarpus stellatus

MEMA Membranipora membranacea

MOMO Modiolus modiolus

MYED Mytilus edulis

OBSP Obelia

OSED Ostrea edulis

PAPA Palmaria palmata

PHRU Phycodrys rubens

PHSP Phymatolithon

POLS Polysiphonia
|
term
|
statistic
|
df
|
p.value
|
|
YEAR
|
1277.926
|
1
|
0
|
|
SITE
|
43350.015
|
2
|
0
|
|
YEAR:SITE
|
42899.533
|
2
|
0
|
PORO Polyides rotunda

PORS Porphyra

PTSE Ptilota serrata

RAT Red Algal Turf

SADE Saccorhiza dermatodea

SCUN Schizoporella unicornis

SE Thylacodes

SL Saccharina latissima
|
term
|
statistic
|
df
|
p.value
|
|
YEAR
|
5505.378
|
1
|
0
|
|
SITE
|
207.203
|
2
|
0
|
|
YEAR:SITE
|
193.902
|
2
|
0
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SLJ Saccharina latissima

SPRE Spermothamnion repens

TETE Testudinalia testudinalis

TISP Titanoderma

TRIN Tricellaria inopinata

TUV Tubular Ulvoid

UEC Unidentified Erect Coralline

UFR Unidentified Filamentous Red

URB Unidentified Red Blade

UV Blady Ulvoid
